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- PDB-7d12: NMR solution structures of CAG RNA-DB213 binding complex -

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Basic information

Entry
Database: PDB / ID: 7d12
TitleNMR solution structures of CAG RNA-DB213 binding complex
ComponentsRNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*CP*UP*UP*CP*GP*GP*CP*AP*GP*CP*AP*GP*C)-3')
KeywordsRNA / CAG RNA / Ligand / Complex
Function / homologyChem-L94 / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChan, H.Y.E. / Guo, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: CAG RNAs induce DNA damage and apoptosis by silencing NUDT16 expression in polyglutamine degeneration.
Authors: Peng, S. / Guo, P. / Lin, X. / An, Y. / Sze, K.H. / Lau, M.H.Y. / Chen, Z.S. / Wang, Q. / Li, W. / Sun, J.K. / Ma, S.Y. / Chan, T.F. / Lau, K.F. / Ngo, J.C.K. / Kwan, K.M. / Wong, C.H. / ...Authors: Peng, S. / Guo, P. / Lin, X. / An, Y. / Sze, K.H. / Lau, M.H.Y. / Chen, Z.S. / Wang, Q. / Li, W. / Sun, J.K. / Ma, S.Y. / Chan, T.F. / Lau, K.F. / Ngo, J.C.K. / Kwan, K.M. / Wong, C.H. / Lam, S.L. / Zimmerman, S.C. / Tuccinardi, T. / Zuo, Z. / Au-Yeung, H.Y. / Chow, H.M. / Chan, H.Y.E.
History
DepositionSep 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*CP*UP*UP*CP*GP*GP*CP*AP*GP*CP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,11817
Polymers6,4371
Non-polymers68116
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1220 Å2
ΔGint-96 kcal/mol
Surface area4550 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*CP*UP*UP*CP*GP*GP*CP*AP*GP*CP*AP*GP*C)-3')


Mass: 6436.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-L94 / N'-{(Z)-amino[4-(amino{[3-(dimethylammonio)propyl]iminio}methyl)phenyl]methylidene}-N,N-dimethylpropane-1,3-diaminium


Mass: 336.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H COSY

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Sample preparation

DetailsType: solution
Contents: 0.4 mM No RNA, 0.4 mM No Ligand, 10.0 mM No NaPi, 0.02 mM No DSS, 0.1 mM No EDTA, 100% D2O
Details: 0.4 mM RNA, 0.4 mM ligand DB213, 10 mM NaPi (pH 7), 0.02 mM DSS, 0.1 mM EDTA.
Label: No label / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMRNANo1
0.4 mMLigandNo1
10.0 mMNaPiNo1
0.02 mMDSSNo1
0.1 mMEDTANo1
Sample conditionsIonic strength: 10.0 mM / Ionic strength err: 0.1 / Label: Condition_1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 bar / Pressure err: 0.01 / Temperature: 283 K / Temperature err: 0.2

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
TopSpinBruker Biospinchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 5

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